We have now both worked more than 5 years in the UK and could apply for ILR.
No you couldn't! You could apply for confirmation of PR ... Permanent Residence .... but you really should not confuse ILR and PR.
This is particularly important these days given that applicants for ILR need to have passed the Life in the UK Citizenship test, but there is no such requirement in the EU regulations relating to PR.
Also appreciate that, based upon what you say, both of you already have PR status in the UK! That came about automatically with the mere passage of time. You got that on the 5th anniversary of starting to use EU Treaty Rights in the UK, or on 30.04.06, whichever came later. 30.04.06? The date new EU regulations came into force, which made significant changes to the EU regulations.
So what do the applications on EEA3 and EEA4 actually do? They get you confirmation of the PR status already held. Nevertheless that is useful, particularly for a non-EEA citizen.
Suggest you you submit a form EEA3 and your wife a form EEA4. Send them in together ... your application will help your wife's ... and enclose photocopies of the passports .... name/pic page and also of any relevant sticker in the passport. Enclose a covering letter explaining that the passports are needed for imminent travel, but can be supplied later if really required.
Acknowledgment letters received back will confirm the continuing ability to work in the UK. Your wife especially should carry a photocopy of her acknowledgment letter whenever she travels abroad.
